Respiratory rhythmogenesis is a term describing the processes for breath generation and patterning over time; abnormal rhythmogenesis carries consequences of hypoxia and hypercapnia, driving morbidity in conditions like sleep apnea, heart failure, stroke, and other chronic neurologic diseases. The C57Bl/6 (B6) mouse has inherent traits of pauses in breathing at rest and post-hypoxic periodic breathing (abnormal rhythmogenesis), localized to a ~50 Mb region on mouse Chromosome 1 which we call the Stab1 (for stability phenotype) QTL. The next step is to further define the functional genomic elements. Based on these novel findings, the hypotheses are that the stability phenotype (Stab1) trait and gene are correlated to hypoxic and/or hypercapnic responsiveness, and that the stability phenotype is expressed through brainstem circuits. Two interrelated aims expand the phenotype and genetic profiling through the opportunities afforded by publically available recombinant inbred strains (RISs) derived from DBA and B6 mouse strains in order to uncover the functions of Stab1 and other novel genes in respiratory rhythmogenesis, breath patterning, and chemosensitivity, in general. Aim 1 is designed to identify Stab1 candidate genes and functional proteins by 1) defining the association of the phenotypic trait of instability (number of pauses >1/minute during resting breathing and/or appearance of >3 cycles of periodic breathing following 2 minutes of hypoxia) with RIS genotypes relative to mRNA expression, and 2) comparing findings to hypoxic and and hypercapnic ventilatory responsiveness. To assess gene functions, we will link RIS genotype to global brainstem mRNA expression. The purpose here is to harness the power of these RISs which are already SNP genotyped, creating the opportunity for a virtual QTL linkage of SNPs to trait expression, and to use global mRNA expression (eQTL) and proteomics to test the hypothesis, identify novel molecular pathways involved in respiratory rhythmogenesis, and offer the opportunity for association studies in humans. Aim 2 will identify mechanisms producing breathing instability in in vitro brainstem slices. Studies test the hypotheses that 1) responses to serotonin agonists and antagonists and 2) responses to opiods, opiod antagonists, and NOS antagonists will disclose dynamic behaviors and circuit components which differ according to strain. The purpose is to utilize the discovery of the B6 instability phenotype as a platform to identify genomic contributions to breathing stability and respiratory control in general, with the long-term goal of mechanistically investigating how genes operate to produce abnormal ventilatory traits. Results from both Aims will inform the design of and priorities for sequencing of candidate genes, for understanding the current limitations of pharmacologic therapy, and for using genes as risk factors in human diseases of respiratory control.